War of Secrets
by Lighting wolf knight
Summary: We all know how the Clone Wars ended, but what if events had been differently? How would the have ended if Clones were around before episode 2? If Sidious was known about? Rated T for Violence, death and profanity. Chapters on Mondays. This chapter is 900 words. On hold after 2 more chapters.
1. Invasion of Naboo

**Summary/disclaimer: Time for another chapter of War of Secrets. Enjoy the 1000 chapter. I don't own Star Wars, Disney and Lucas Films do.**

 **(** _ **Guardian**_ **, Naboo System, 28 BBC.)**

The _Guardian_ was a new Warship, it wasn't the first of its kind and it wouldn't be the last of its kind.

That wasn't on the mind of the two Jedi who commanded the warship on its mission.

These would be Jedi Master Tiplee and her apprentice: Dernat Beltoll, a Togruta with an eye for Tactics.

Tiplee turned to see her apprentice writing in a Holo journal, something he usually did.

"Dernat."

The Jedi Master called as he and his Clone Captain: Spark, turned to look at her.

"Yes, master?"

Dernat asked as Tiplee walked to the bridge window, the Mikkian Jedi Master and her Padawan had been sent along with the 449th Clone Legion, and Dernat's 388th Clone Corps had been sent if conflict broke out.

"I sense conflict will be coming to Naboo soon… Master Qui-Gon Jinn and Obi-Wan Kenobi will be in danger soon."

Tiplee put in, there was dozens of Clones on the bridge, Dernat's clones wore Sliver markings and Tiplee's had Crimson markings on their Phase 1 armor.

Dernat and Spark shared a look before Dernat turned to Tiplee and spoke up.

"If that's the case, me and Captain Spark should go to the hanger bay and organize the troops… I wish the Council had sent us with more than 1 ship…"

Dernat muttered, he understood sending a Clone Army to Naboo alongside 2 Jedi Masters.

But the _Guardian_ was outgunned by the _Profiteer_ which had blockaded the planet, it was meant for landing soldiers and equipment on the battlefield, not for orbital combat with a battleship.

 **(** _ **Guardian**_ **Hanger bay, 10 minutes later.)**

There wasn't a signal that things had gone wrong, but the fact that the _Radiant VII_ was destroyed had been a big enough warning to the _Guardian_ that things had gone badly.

The Vulture Droid waves being launched at them also helped. Dernat and Spark ordered 5 LAAT Gunships to be launched from _Guardian_ while it held off the Vulture Droids with its laser cannons.

The 5 Gunships that held 149 Clones and Dernat broke through the clouds of Naboo and landed on the plains.

"Spread out, we have no idea how many droids the Trade Federation is going to land."

Dernat ordered, he wished the _Guardian_ had been able to launch more LAATs then 5, there was more droids then Clones on the planet.

Dernat led his Company of Clones towards Theed, they couldn't advance by air, the Vulture Droids would cut them down before they would've been able to reach the city.

They were cut off by about 100 Battle Droids and 4 AATs advancing on them, forcing them to take cover behind rocks.

"Thin out the Battle Droids, Ill handle the tanks, Captain."

Dernat ordered as his Clones began to fire upon the rows of B1 Battle Droids as Dernat ignited his Blue Bladed Lightsaber and charged the four AATs, he force pushed a squad of B1s into a rock, destroying them as he leapt onto an AAT.

He sliced the cannon off 1 Tank and then leapt off it as the other tanks fired, destroying the tank.

He landed on the second tank and sliced it in half at the front, he flipped off the tank and ran towards the third tank, sliding under it and slicing it in half.

He was about to deal with the 4th AAT when it blew into pieces, a LAAT flew overhead, firing on the rows of Battle Droids that his Clone Troopers hadn't taken out.

"General, the droids are being marched to Theed, _Guardian_ sent every Gunship it had and jumped out of the system…. For now, we're on our own against the clankers."

One of the Clones on the Gunship explained, Dernat looked up at the Gunship, another wave of them were being sent to Theed, Dernat couldn't tell how many droids were already sent to the planet or how many Vulture Droids were around at the moment.

"Where's Master Tiplee?"

Dernat asked, he didn't know how much time they'd have to organize a defense of the planet.

"General Tiplee is searching for Master Kenobi and Master Jinn in the forest…. What are your orders, General?"

The Clone asked before Dernat turned to see rows of B1 Battle Droids and AATS marching towards them.

They wouldn't be able to stop the takeover of Theed, there was too many to stop with such a small army, not against a Droid Battleship, at least.

"Land as many troops as you can, we hold off the Droid Army until Master Tiplee comes back."

Dernat ordered, the Clones readied themselves for battle against the waves of droids.

 **(With Master Tiplee and Commander Doom.)**

Master Tiplee wished she had ordered Dernat and his Army to stay put, he might have been a Jedi Knight, but he was still young.

She could hear the sounds of Blaster Fire in the distance, Dernat and his army were probably engaging the Trade Federation's Invasion forces.

"Commander, have you spotted them yet?"

Tiplee asked, Dernat and his forces wouldn't be able to hold off the Droids for long, not with a Battleship in orbit and with no forces to challenge them in orbit.

"Not yet, General, we're keep looking… We aren't going to be able to hold off the Clankers, they have too many numbers… We're going to need reinforcements…"

Doom put in, Tiplee couldn't agree more.

She wondered how her apprentice was doing.

 **Author notes**

 **Phew, first chapter done! Yes, I know it isn't perfect, first chapters aren't my thing. As for Clones being on Naboo? And Jedi being in Episode 1? My story is a retelling of the Clone Wars and how the Clone Wars could have gone if events had been different. Next chapter will be Thursday and will show Dernat and his army fighting the Droid Army. Until then, Lighting Wolf Out!**


	2. Republic Regrouping

**Summary/disclaimer: Time for another chapter of War of Secrets. Enjoy the 1500 chapter. I don't own Star Wars, Disney and Lucas Films do.**

 **(Naboo, 28 BBC.)**

Another AAT exploded into pieces as more and more B1 Battle Droids were cut down by Dernat's Clone Troopers, the Jedi Knight continued to led his soldiers towards the safety of the city.

"Keep falling back, we can't face the droids head on!"

Dernat ordered his army, he and his Troops finally were able to find decent cover on the edge of the forest.

Dernat had lost 30 Clones to the Droids, he sighed and watched as the Droids and their Tanks marched into the city, he could only hope Master Tiplee had found Master Qui-Gon and Obi- Wan.

He and the hundreds of Clones of the 388th took cover in the woods, some of them were wondering why the Droids didn't send troops to wipe them out.

Dernat knew better, they wanted to capture the city and then deal with other forces on the planet.

Dernat wondered how many of their forces were able to reach the planet, they would need walkers and mechanized forces to counter the dozens of AATs, MTTs and STAPs the Trade Federation had brought with them to the planet.

"You said _Guardian_ fled the system? _"_

Dernat asked Spark who stepped up to the Jedi General and nodded while looking around for Battle Droids.

"Yes, General…. The ship fled the system after she deployed every LAAT she had aboard… They couldn't stand up to an entire fleet of battleships…."

Spark stated, causing Dernat to sigh, without anything in orbit to oppose the blockade, they were trapped, and even if they wiped out every Battle Droid in the invasion army, they wouldn't be able to deal with the 5 battleships in orbit.

"Damn it, that limits our options…. See how many speeders and walkers managed to make it to the surface, Captain…. Make a camp here, I'll come up with a plan to deal with the Trade Federation army."

Dernat ordered, he was cut off by a voice from behind him, dozens of clones moved out of the way.

"There you are, Dernat…. Are you ok?"

Tiplee said from behind Dernat as he turned to the Jedi Master.

"Master Tiplee, you're ok…. We're fine, we can't fight the Droids head on… We've regrouped here for now."

Dernat explained, the rest of his clones started looking around, searching for droids to deal with.

"How many walkers survived, Captain?"

Dernat asked when Spark walked back with his DC-15S which he rested on his shoulder.

"Little more than a dozen AT-TEs, a dozen or so Swamp Speeders and one squadron of BARC speeders."

The Clone Captain explained, Dernat sighed and leapt off the tree, landing in the Swamp Water.

"Ok then…. Come with me, I'll try and come up with a battle plan…"

Dernat muttered, he led the Clone Captain into the depths of the swamp.

 **(Republic Camp, 10 minutes later.)**

Dernat knew his master wouldn't be back when he came back to the spot where she had been, she would probably go to aid Master Qui-Gon and Obi-Wan.

"We don't have the numbers or firepower to challenge the Droids head on, General, what did you suppose we do?"

Spark asked, Dernat looked up at the sky, there was a makeshift landing pad being set up and all that, Dernat looked at his forces before turning to Spark.

"Send out a squad of ARF Troopers to find out what they can about the Invasion forces…. We will have to face them on the plains, we can't invade the city without causing casualties and fighting the droids on their home turf…. But the problem with facing the droids on the plains is they outgun us… And we have no cover to deal with the droids…. Plus, we have to deal with the blockade or their just reinforce their ground forces…"

Dernat muttered, Spark nodded, he and Dernat liked to deal with the enemy directly, but they couldn't, not in this case and not with a blockade that could just reinforce them the second they let their guard down.

"I'll get right on that, General… Anything else? The clankers can't be that dug in at Theed, they might be strong in number, but they aren't the smartest bunch around…. Plus, there's no way they can keep track of us without patrols…."

Spark muttered, Dernat crossed his arms, he decided to do some recon of his own.

"True…. I'll be back in an hour or so, Captain…. I want to check on something… Make sure our defenses are shored up…"

Dernat ordered as well, he walked toward a squad of his ARC troopers.

He had an idea that he could use if the ARC troopers and his squad of soldiers would be able to complete their mission.

 **(Great Grassy Plains, 2 hours later.)**

Dernat and his squad of ARC Troopers sped across the plains on their speeder bikes, they were going to recon the Trade Federation's landing zone and see if they could figure out a battle plan.

In truth, Dernat already had a battle plan to deal with the droid army, it was the AATs, MTTs and STAPs that would be the problem and Dernat had a plan to take out that mechanized force, provided that the BARC Speeders survived the recon mission.

"Stop here."

Dernat ordered, stopping his speeder bike as the 5 ARC troopers behind him did the same.

"Remember, this is a recon mission…. We only fight if we get spotted…. If we can sabotage their forces, that's secondary…. We can't take on their forces while they're in Theed or we risk killing the Naboo…."

Dernat muttered, he wished he could have dug in his army into the plains, if they had, they probably would have been able to rout or even destroy the entire invasion army.

Then it would have been a simple matter of arresting the Viceroy and handling the blockade.

Dernat was cut off as they managed to crawl to a ledge, he took a pair of Macrobinoculars off his belt and used them to zoom in on a C-9979 Landing Ship.

He saw a row of MTTs and B1 Battle Droids descending the ramp, a squadron of AATs joined them.

"Reinforcements?"

One of the Arc Troopers asked, readying his DC-15A in preparation for battle if it was needed.

"No, another army…. We need to take out their blockade or their land enough droids to slaughter any army we bring…"

Dernat muttered, they didn't notice the ship rising from Theed and taking off, if they had, they would have known it was carrying the queen and the other Jedi.

Dernat however, was too busy observing the Droid forces to notice the slight disturbance in the force.

"Sir, I believe the blockade is moving."

One of the ARC Troopers stated, he craned his head and switched his viewfinder to its max.

"What? Are you sure?"

Dernat muttered, he wished he had a squad of Clone Commandos with him, they would have been able to take out the landing zone without drawing attention…

"Yes, all but one of their battleships just left to hyperspace…. They were shooting at something but it was too fast for me to get a read on it right."

"Hmm…. Let's return to the camp, if they've removed all but their command ship, it means they've grown lax…. The Viceroy probably believes one battleship and its troops can handle us…"

Dernat muttered, he and his squad of Troopers made their way back to their BARC speeders and sped back to the Republic swamp camp.

 **(Republic Camp, 15 minutes later.)**

Dernat used a AT-TE as his command center and looked at its onboard Holoprojecter.

"All but the _Vuutun Palaa_ have left Naboo's orbit… And I don't sense Master Tiplee, Spark… She and the others must have escaped with the queen, she's the only one the Viceroy would worry about… That aids us."

Dernat muttered, Spark put his helmet under his shoulder.

"That still leaves over a thousand clankers to deal with…. We don't entirely have enough men… I suppose we hunker down for now?"

Spark suggested, Dernat nodded and turned back to the holoprojecter.

"Yes, we wait for General Tiplee to return… But, we should get ready for the battle, our next move will decide things…. Get some trenches dug outside on the smaller hills and make sure the AT-TEs and other walkers are combat worthy…."

Dernat muttered, he had a plan to deal with the Droid Army now.

He just needed to lure them to the plains.

 **Author notes**

 **Phew, another chapter done! Yes, I know this arc on Naboo is going faster then it should but that's because I want to get to other battles in the story. This story changes the entire first 3 movies. Next chapter will show Dernat's army and the Gungans facing the droid army and will take place 2 days after the events of this chapter. Until next, next Tuesdays. Lighting Wolf out!**


	3. Battle of Naboo

**Summary/disclaimer: Time for another chapter of War of Secrets. Enjoy the 900-chapter. I don't own Star Wars, Disney and Lucas Films do.**

 **(Naboo, 28 BBC.)**

Dernat sensed his master and the other Jedi before he saw them again.

He turned to face them as his Clone Troopers parted to let the Jedi Master and General through.

"Dernat, you've been here all this time?"

Tiplee asked, Dernat turned to Spark and motioned for him to go to the AT-TEs.

"We've been here the whole time… I was just about to explain the battle plan… I just needed to draw the Droid Army out from Theed..."

Dernat muttered, Tiplee walked to lean on one of the trees before looking at her apprentice soon again.

"I believe Master Qui-Gon and Master Obi-Wan can handle that…. I'm going to capture the palace with Commander Doom, the Queen and Master Qui-Gon and Obi-Wan…"

Tiplee muttered, Dernat chuckled and turned to face her.

"Well, lay it on me, Master…. I'll explain the plan after you fill me in…."

Dernat stated while Tiplee smiled and walked over to explain the plan she and the others had come up with.

 **(15 minutes later.)**

Dernat and Tiplee had come with a brilliant military plan, Spark would hear it in a second.

"Ok, here's the plan…"

Dernat started to say, he looked at his army before starting to explain the plan.

"The Gungans will directly confront the Trade Federation's army head on… We will ambush the droids from one of the lower hills from the trenches…. The AT-TEs will target the AATs and MTTs in their ranks while the infantry deal with the Droid infantry… The trenches will give us cover from the droids."

Dernat explained, pointing at the holoprojecter to explain his plan, some of the clones looked unsure.

"What about that battleship in orbit, General? We can't take that out of the sky."

One of the Clones stated, the Jedi General chuckled before turning back to the holoprojecter.

"The Naboo will deal with that, General Tiplee said the Naboo are trying to get ahold of a group of N-1 Starfighters in orbit… All we have to do deal with the clankers on the battlefield, Captain…"

Dernat muttered before giving on one last rallying call to his forces.

"Let's scrap some clankers, boys!"

Dernat yelled as his clones cheered and waved their blasters in the air.

"Let's end this…"

Dernat muttered before turning back to the plain to lead his army to victory… And he knew just how he would start off the battle.

 **(Great Grass Plains, 10 minutes later.)**

Dernat had placed Spark in charge of the AT-TEs and AT-RTs in the army, he hadn't known where Dernat had gone, but he had told Spark that he would know when to open fire on the droids when he saw it.

"Should we ambush the clankers now?"

One of the clones next to Spark asked, the Clone Captain shook his head, Dernat had proved himself to be a good general in combat, Spark knew better then to try another plan.

Little did he know, Dernat would handle the droid tanks head on.

He nodded to his ARC Troopers on the BARC Speeder Bikes and both the Swamp Speeder and AT-RTs.

"Hit the armor first, then blast your way back to the front lines, now!"

Dernat yelled while charging the Trade Federation's ranks, he pulled a small sliver orb off his belt and chucked it at the first MTT which happened to get in his way.

The thermal detonator was joined by others from the other BARC Speeder clones who fired at the Battle Droids as they passed.

"SPARK, HIT THEM NOW!"

Dernat ordered, he sliced an AAT's gun off as he passed, he saw blasts coming from his infantry and AT-TEs, they blew up two of the incoming ATTs as the detonators exploded.

The 12 MTTs and 4 of the AATs exploded into scrap metal, his Clones began to gun down the B1 Battle Droids as Dernat fired the guns of his BARC Speeder.

"General, the plans working, they've lost most of their armor and we've already started destroying their infantry!"

Spark reported as a STAP exploded, Dernat was preparing to make another pass when the droids stopped moving, he looked up.

"General?"

One of the Clones asked as Dernat and the others looked up at the sky.

The Trade Federation Battleship had exploded into pieces and was crashing back down onto the planet.

"Their control signal is gone, that means the droids will shut down… That must also mean Master Tiplee captured Theed, Captain…"

Dernat muttered, he felt off, like something awful had happened.

 **(In Theed, 20 minutes later.)**

Dernat had taken a LAAT Gunship to Theed, Spark and his men had stayed to make sure the droids were dealt with for good.

"Coming up on the city now, General… Doesn't look like they had as much of a fight as we did."

Dernat heard from his pilot, he was silent, he felt a void in the force.

A Jedi had fallen, and a Sith had been present.

 **Author notes**

 **Phew, another chapter done! Yes, this chapter is shorter than the others, I didn't have much to write and I wanted to be able to move onto new battles. Next chapter will take place a few months later and will show Dernat and Spark looking over the aftermath of the battle back home.**


	4. Republic War meeting

**Summary/disclaimer: Time for another chapter of War of Secrets. Enjoy the 800-chapter. I don't own Star Wars, Disney and Lucas Films do.**

 **(** _ **Spearpoint**_ **22 BBC.)**

Spark found his General in the war room, if he wasn't in a military base, he was almost always in the war room of his flagship.

"General, your still here?"

Spark asked, Dernat said something to one of his Clone officers and turned to his lieutenant a second later.

"I've been going over reports of Separatist Activity, Commander… They've been quiet ever since Naboo…"

The Jedi Knight stated, both Republic officers turned back to the holotable with a frown visible on both of their faces.

"They must be mustering forces for an invasion…. Seppies are never act like this, though…. You want me to round up the boys and go on a scouting mission?"

Spark asked, Dernat shook his head, he might have had a fleet and he might have had troops to spare but sending his second in command away when Dernat needed him wouldn't help anyone.

"No, I need you here…. This is unusual, though… Lieutenant, have we intercepted any transmissions lately? Doesn't matter what kind, just any from an unknown party?"

Dernat asked, the Jedi General wanted another victory against the Separatists, it would give the Republic time to regroup, not that they haven't already, considering all the years that it had been.

"No, General, we haven't intercepted any transmissions yet… But we have intercepted a fleet of cargo frigates headed to one of the moons in the Geonosis system…"

One of the Clone Navel Officers reported, he tapped a few keys on the Holotable and it brought up a layout of the system.

Spark and Dernat did note the stream of cargo ships passing through the system, it was supposed to be abandoned, the Geonosians weren't known for sharing their technology.

"Commander, get _Gundark_ squad and send them in… And then contact General Tiplee and fill her and the council in…. If that moon is doing what I'm assuming they are, then we should deal with them while we can…."

Dernat ordered, Spark nodded and left the bridge, he would also make sure the 388th were ready incase Dernat decided to bring in all of his forces.

"And Commander? Join them… Take the _Guardian_ and see what you can find, if there's anything hiding there, I want to be able to strike right away… I'll have the _Spearpoint_ join you if you run into any Clankers…."

Dernat muttered, Spark smiled and nodded, he had no business commanding a warship, but he knew that Dernat would want his troops to be able to strike as soon as possible, it was what Clones like him were trained for.

"I'll get it done, General…. I'm guessing you don't want to report to General Tiplee then?"

Spark asked, Dernat turned to one of his Clone officers who nodded and left the room.

"There's your answer, Commander…. Ill be along with reinforcements to reinforce you at the first sign of any trouble…. Happy hunting."

Dernat stated with a laugh, Spark saluted and left the room, going to the hanger bay would give him a sign to think considering he had the wait from the LAAT to the _Guardian_ to prepare for the mission his General had given him.

"It's going to be fun… Been a few years since I've blasted a few clankers."

Spark said with a smile as he climbed into a LAAT and rode towards the _Acclamator_ -class Assault Ship.

 **(** _ **Spearpoint**_ **bridge, 20 minutes later.)**

Dernat hummed and planned his next move as the _Guardian_ , he should have sent more forces to reinforce his Lieutenant, but he knew Spark could and would be able to handle himself without backup, he turned back to the Holotable and hummed once more.

"Where are you hiding, Count?"

Dernat asked himself at the moment, he switched to a tactical view to show his fleet.

4 Venator-class Cruisers/carriers, 6 Arquiten-class Light Cruisers and 6 Consular-class Light Cruisers.

Not entirely the strongest military force in the galaxy, but it would do, he just wanted a report sent to the rest of the Jedi Council and then he would leave.

"Ain't no sense coming in blasters blazing and not have them know about it in the first place…."

Dernat muttered, he turned to the viewport and walked through the doors to the bridge.

This war was just beginning and he and the Republic had to make the first move.

 **Author notes**

 **Phew, another chapter done! Yes, this will be the last chapter for now, I didn't know where else to bring this story, plus I have moved onto other stories for the moment, I will return to this story soon, but not now or anytime down the road. Until next chapter, Lighting Wolf out!**


End file.
